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RocklinC

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A python module for performing Rocklin Correction.

Installing from source

from source. Clone the source from GitHub with::

git clone https://github.com/xiki-tempula/rocklinc.git

then do::

cd rocklinc
pip install .

Uasge

To compute Rocklin correction. The following data is required.

  • u: MDAnalysis.Universe object that contains positions, charges, radii and dimensions.
  • box: The dimension (Å) of the simulation box in the form of a list (e.g. [100, 100, 100]).
  • lig_netq: The total charge of the ligand.
  • protein_netq: The total charge of the rest of the system excluding ligand.
  • temp: The temperature of the simulation (K).
  • water: The water model being used. Only rocklinc.waters.TIP3P and rocklinc.waters.TIP4P are supported for now.
  • lig_selection: The MDAnalysis selection string for the ligand.
  • apbs_exe: The executable path of the APBS software.

A full automatic calculation of Rocklin correction could be performed with:

    import rocklinc
    correction = rocklinc.RocklinCorrection(box, lig_netq, protein_netq, temp)
    correction.make_APBS_input(u, lig_selection)
    correction.run_APBS(apbs_exe=apbs_exe)
    correction.read_APBS()
    result = correction.compute()
    correction.write('correction.txt')

result is the correction energy, while the details are written in 'correction.txt'.

Please see the full documentation from RTD. https://rocklinc.readthedocs.io/

Copyright

Copyright (c) 2020, Zhiyi Wu

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.3.